• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.21 no.8
• /
• pp.417-428
• /
• 2020

Housekeeping genes are expressed in cells of all organisms and perform basic cellular functions such as energy generation, substance synthesis, cell death, and cell defense. Accordingly, the expression levels of housekeeping genes are relatively constant, and thus they are used as reference genes in gene expression studies, such as protein expression and mRNA expression analysis of target genes. However, the levels of expression of these genes may be different among various tissues or cells and may change under certain circumstances. Therefore, it is important to select the best reference gene for specific gene expression research by exploring the stability of housekeeping gene expression. This review summarizes housekeeping genes found in humans, chickens, pigs, and rats in the literature and estimates expression stability using geNorm, NormFinder, and BestKeeper software. The most suitable reference housekeeping gene can selected based on expression stability according to the experimental conditions of the gene expression study and can thus be applied to data normalization.

• Research in Plant Disease
• /
• v.16 no.3
• /
• pp.312-315
• /
• 2010

Pectobacterium carotovorum subsp. carotovorum (Pcc) causes soft rot disease in various plants. Although many studies about Pcc have been going on, little is known yet about the defense genes from plants. To identify defense associated genes in response to Pcc, we screened about 20 thousand Arabidopsis T-DNA knock out lines by inoculation with Pcc. We obtained a line (Atspt1) showing more susceptible symptom compared to WT (Col-0) on 1 day after the inoculation of Pcc on leaves of Arabidopsis with toothpicks. In this study, we optimized the system to select resistant and susceptible lines to Pcc from T-DNA inserted pool of Arabidopsis and expect the system and Atspt1 might be used for molecular breeding to produce resistant vegetables against Pcc.

• Proceedings of the Korean Society of Plant Pathology Conference
• /
• 2004.10a
• /
• pp.65-67
• /
• 2004

During initial interactions of bacteria with their host plants, most plants recognize the bacterial infections and repel the pathogen by plant defense mechanism. The most active plant defense mechanism is the hypersensitive response (HR) which is the localized induced cell death in the plant at the site of infection by a pathogen. A primary locus induced in gram-negative phytopathogenic bacteria during this initial interaction is the Hrp locus. The Hrp locus is composed of a cluster of genes that encodes the bacteral Type 111 machinery that is involved in the secretion and translocation of effector proteins to the plant cell. DNA sequence analysis of hrp gene in phytopathogenic bacteria has revealed a Hrp pathogenicity is]and (PAI) with a tripartite mosaic structure. For many gram-negative pathogenic bacteria, colonization of the host's tissue depends on the type III protein secretion system (TTSS) which secrets and translocates effector proteins into the host cell. Effectors can be divided into several groups including broad host range effectors, host specific effectors, disease specific effectors, and effectors inhibit host defenses. The role of effectors carrying LRR domain in plant resistance is very elusive since most known plant resistance gene carry LRR domain. Host specific effectors such as several avr gene products are involved in the determination of the host specificity. Almost all the phytopathogenic Xanthomonas spp. carry avrBs1, avrBs2, and avrBs3 homologs. Some strains of X. oryzae pv. oryzae carry more than 10 copies of avrBs3 homologs. However, the functions of all those avr genes in host specificity are not characterized well.;

• Journal of Microbiology and Biotechnology
• /
• v.26 no.9
• /
• pp.1542-1550
• /
• 2016

This is the first report that paromomycin, an antibiotic derived from Streptomyces sp. AG-P 1441 (AG-P 1441), controlled Phytophthora blight and soft rot diseases caused by Phytophthora capsici and Pectobacterium carotovorum, respectively, in chili pepper (Capsicum annum L.). Chili pepper plants treated with paromomycin by foliar spray or soil drenching 7 days prior to inoculation with P. capsici zoospores showed significant (p < 0.05) reduction in disease severity (%) when compared with untreated control plants. The disease severity of Phytophthora blight was recorded as 8% and 50% for foliar spray and soil drench, respectively, at 1.0 ppm of paromomycin, compared with untreated control, where disease severity was 83% and 100% by foliar spray and soil drench, respectively. A greater reduction of soft rot lesion areas per leaf disk was observed in treated plants using paromomycin (1.0 μg/ml) by infiltration or soil drench in comparison with untreated control plants. Paromomycin treatment did not negatively affect the growth of chili pepper. Furthermore, the treatment slightly promoted growth; this growth was supported by increased chlorophyll content in paromomycin-treated chili pepper plants. Additionally, paromomycin likely induced resistance as confirmed by the expression of pathogenesis-related (PR) genes: PR-1, β-1,3-glucanase, chitinase, PR-4, peroxidase, and PR-10, which enhanced plant defense against P. capsici in chili pepper. This finding indicates that AG-P 1441 plays a role in pathogen resistance upon the activation of defense genes, by secretion of the plant resistance elicitor, paromomycin.

• Molecules and Cells
• /
• v.19 no.3
• /
• pp.418-427
• /
• 2005

When inoculated into sensitive tobacco Xanthi-nn plants, the crucifer and garlic-infecting Tobacco mosaic virus (TMV-Cg) induces local necrotic lesions that resemble those seen in the hypersensitive response (HR) of resistant tobacco plants. However, unlike these, tobacco Xanthi-nn plants do not become resistant to infection and the virus spreads systemically causing a severe disease characterized by necrotic lesions throughout the plant. To identify the viral protein that elicits this necrotic response, we used a set of hybrid viruses constructed by combination of TMV-Cg and the tobacco mosaic virus strain U1 (TMV-U1). In this study we present evidence that the coat protein of TMV-Cg (CPCg) is the elicitor of the necrotic response in tobacco Xanthi-nn plants. Local and systemic necrotic lesions induced by TMV-Cg and by the hybrid U1-CPCg -that carries CPCg in a TMV-U1 context- are characterized by cell death and by the presence of autoflorescent phenolic compounds and $H_2O_2$, just like the HR lesions. In addition, defense-related genes and detoxifying genes are induced in tobacco Xanthi-nn plants after TMV-Cg and U1-CPCg inoculation. We postulate that in our system, CPCg is recognized by sensitive tobacco plants that mount an incomplete defense response. We call this an HR-like since it is not enough to induce plant resistance.

• Journal of the Korea Institute of Military Science and Technology
• /
• v.18 no.4
• /
• pp.478-483
• /
• 2015

Decontamination of biological agents utilizes hydrogen peroxide($H_2O_2$) for its effectiveness and safeness. Bacillus anthracis is a major target for $H_2O_2$ decontamination. To assess the effect of $H_2O_2$ on B. anthracis and identify biomarkers for decontamination, whole transcriptomic profiling of $H_2O_2$-treated B. anthracis was performed. Here we identified deregulation in stress response genes, transcription factors and cellular homeostasis genes. We also found that expression of antisense RNAs increased in B. anthracis during decontamination. We postulate that B. anthracis prioritizes survival and adaptation in response to $H_2O_2$ treatment by changing its gene expression pattern.

• Research in Plant Disease
• /
• v.26 no.3
• /
• pp.144-158
• /
• 2020

Quantitative reverse transcription PCR is used for gene expression analysis as the accurate and sensitive method. To analyze quantification of gene expression changes in apple plants, 10 housekeeping genes (ACT, CKL, EF-1α, GAPDH, MDH, PDI, THFs, UBC, UBC10, and WD40) were evaluated for their stability of expression during infection by Apple stem grooving virus (ASGV) or in cold-stress apple plant buds. Five reference-gene validation programs were used to establish the order of the most stable genes for ASGV as CKL>THFs>GAPDH>ACT, and the least stable genes WD40CKL>UBC10, and the least stable genes were ACT

• Korean Journal of Poultry Science
• /
• v.47 no.1
• /
• pp.9-19
• /
• 2020

Avian influenza (AI) viruses are highly contagious viruses that infect many bird species and are zoonotic. Ducks are resistant to the deadly and highly pathogenic avian influenza virus (HPAIV) and remain asymptomatic to the low pathogenic avian influenza virus (LPAIV). In this study, we identified common differentially expressed genes (DEGs) after a reanalysis of previous transcriptomic data for the HPAIV and LPAIV infected duck lung cells. Microarray datasets from a previous study were reanalyzed to identify common target genes from DEGs and their biological functions. A total of 731 and 439 DEGs were identified in HPAIV- and LPAIV-infected duck lung cells, respectively. Of these, 227 genes were common to cells infected with both viruses, in which 193 genes were upregulated and 34 genes were downregulated. Functional annotation of common DEGs revealed that translation related gene ontology (GO) terms were enriched, including ribosome, protein metabolism, and gene expression. REACTOME analyses also identified pathways for protein and RNA metabolism as well as for tissue repair, including collagen biosynthesis and modification, suggesting that AIVs may evade the host defense system by suppressing host translation machinery or may be suppressed before being exported to the cytosol for translation. AIV infection also increased collagen synthesis, showing that tissue lesions by virus infection may be mediated by this pathway. Further studies should focus on these genes to clarify their roles in AIV pathogenesis and their possible use in AIV therapeutics.

• The Journal of Internal Korean Medicine
• /
• v.27 no.1
• /
• pp.228-236
• /
• 2006

Objectives : Macrophage has an important innate defense role in the immune system. When we are infected with pathogens, macrophage ingests them through phagocytosis or endocytosis, and then secretes many cytokines, such as IL-1, IL-6 and $TGF{\alpha}$, which are regulators of immune responses. The aim of this study is to determine how Samjunghwan effects the expression of cytokine and other immune-related genes in macrophages. Methods : Cells were treated directly with Samjunghwan and/or LPS at regular intervals. Total RNA of cells was isolated using TRIzol reagent, and the changes in cytokine gene expressions were investigated using RT-PCR, western blot and ELISA. Results : $IL-1{\alpha},\;IL-1{\beta}$ and COX-2 genes were inducibly expressed specifically by Samjunghwan in macrophage. Especially, $IL-1{\beta}$ gene was induced most strongly by treatment with Samjunghwan. Over time, treatment with Samjunghwan showed that the expression levels of $IL-1{\alpha}\;and\;$IL-1{\beta}$ genes increased from 1 to 4h, and then decreased from 4 to ISh. However, the expression level of COX-2 gene increased continuously up to 11h. $IL-1{\alpha},\;IL-1{\beta}$ and COX-2 genes were expressed synergistically by a simultaneous treatment of both Samjunghwan and LPS in macrophages. Secretion levels of translated $IL-1{\beta}$ increased continuously up to 11h. Conclusions : Though this study is only a start in the investigation of the efficasy of Samjunghwan, these results suggest that Samjunghwan has positive effects on immune responses.

• Nutrition Research and Practice
• /
• v.1 no.1
• /
• pp.19-28
• /
• 2007

To identify regulatory molecules which play key roles in the development of obesity, we investigated the transcriptional profiles in 3T3-L1 cells at early stage of differentiation and analyzed the promoter sequences of differentially regulated genes. One hundred and sixty-one (161) genes were found to have significant changes in expression at the 2nd day following treatment with differentiation cocktail. Among them, 86 transcripts were up-regulated and 75 transcripts were down-regulated. The 161 transcripts were classified into 10 categories according to their functional roles; cytoskeleton, cell adhesion, immune, defense response, metabolism, protein modification, protein metabolism, regulation of transcription, signal transduction and transporter. To identify transcription factors likely involved in regulating these differentially expressed genes, we analyzed the promoter sequences of up- or - down regulated genes for the presence of transcription factor binding sites (TFBSs). Based on coincidence of regulatory sites, we have identified candidate transcription factors (TFs), which include those previously known to be involved in adipogenesis (CREB, OCT-1 and c-Myc). Among them, c-Myc was also identified by our microarray data. Our approach to take advantage of the resource of the human genome sequences and the results from our microarray experiments should be validated by further studies of promoter occupancy and TF perturbation.